The effects of process conditions on proteolysis of three recombinant IgG-binding proteins ZT3, ZZT3 and protein A in E. coli were studied. SDS/PAGE shows that the relative amount of degradation intermediates of ZT3 in a shake flask cultivation is much higher than that in a bioreactor culture. The rate of proteolysis of ZZT3 and protein A was also higher in shake flask cultures than in bioreactor cultures. The proteolysis rate constant of ZZT3 was 12/h in a shake flask but only 2.1/h in a bioreactor. Corresponding values for protein A were 2.4/h and 1.0/h, respectively. High proteolysis rate constants correlated with lower product yields.